A statistical mechanics description of environmental variability in metabolic networks

J.J. Crofts, Ernesto Estrada

Research output: Contribution to journalArticle

2 Citations (Scopus)
48 Downloads (Pure)

Abstract

Many of the chemical reactions that take place within a living cell are
irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks display considerable asymmetry. In this paper, we explore possible evolutionary factors pertaining to the reduced symmetry observed in these networks, and demonstrate the important role environmental variability plays in shaping their structural organization. Interpreting the returnability index as an equilibrium constant for a reaction network in equilibrium with a hypothetical reference system, enables us to quantify the extent to which a metabolic network is in disequilibrium. Further, by introducing a new directed centrality measure via an extension of the subgraph centrality metric to directed networks, we are able to characterise individual metabolites by their participation within metabolic pathways. To demonstrate these ideas, we study 116 metabolic networks of bacteria. In particular, we find that the equilibrium constant for the metabolic networks decreases significantly in-line with variability in bacterial habitats, supporting the view that environmental variability promotes disequilibrium
within these biochemical reaction systems
Original languageEnglish
Pages (from-to)675-688
Number of pages14
JournalJournal of Mathematical Chemistry
Volume52
Issue number2
DOIs
Publication statusPublished - Feb 2014

Fingerprint

Statistical mechanics
Metabolic Network
Statistical Mechanics
Centrality
Equilibrium constants
Reaction Network
Directed Network
Chemical Reaction
Bacteria
Demonstrate
Asymmetry
Subgraph
Pathway
Metabolites
Quantify
Chemical reactions
Symmetry
Metric
Decrease
Cells

Keywords

  • complexity
  • metabolic networks
  • returnability
  • centrality
  • statistical mechanics
  • environmental variability

Cite this

@article{233005262a1e4b3fb57ffee699ec943f,
title = "A statistical mechanics description of environmental variability in metabolic networks",
abstract = "Many of the chemical reactions that take place within a living cell areirreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks display considerable asymmetry. In this paper, we explore possible evolutionary factors pertaining to the reduced symmetry observed in these networks, and demonstrate the important role environmental variability plays in shaping their structural organization. Interpreting the returnability index as an equilibrium constant for a reaction network in equilibrium with a hypothetical reference system, enables us to quantify the extent to which a metabolic network is in disequilibrium. Further, by introducing a new directed centrality measure via an extension of the subgraph centrality metric to directed networks, we are able to characterise individual metabolites by their participation within metabolic pathways. To demonstrate these ideas, we study 116 metabolic networks of bacteria. In particular, we find that the equilibrium constant for the metabolic networks decreases significantly in-line with variability in bacterial habitats, supporting the view that environmental variability promotes disequilibriumwithin these biochemical reaction systems",
keywords = "complexity, metabolic networks, returnability, centrality, statistical mechanics, environmental variability",
author = "J.J. Crofts and Ernesto Estrada",
year = "2014",
month = "2",
doi = "10.1007/s10910-013-0288-7",
language = "English",
volume = "52",
pages = "675--688",
journal = "Journal of Mathematical Chemistry",
issn = "0259-9791",
number = "2",

}

A statistical mechanics description of environmental variability in metabolic networks. / Crofts, J.J.; Estrada, Ernesto.

In: Journal of Mathematical Chemistry, Vol. 52, No. 2, 02.2014, p. 675-688.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A statistical mechanics description of environmental variability in metabolic networks

AU - Crofts, J.J.

AU - Estrada, Ernesto

PY - 2014/2

Y1 - 2014/2

N2 - Many of the chemical reactions that take place within a living cell areirreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks display considerable asymmetry. In this paper, we explore possible evolutionary factors pertaining to the reduced symmetry observed in these networks, and demonstrate the important role environmental variability plays in shaping their structural organization. Interpreting the returnability index as an equilibrium constant for a reaction network in equilibrium with a hypothetical reference system, enables us to quantify the extent to which a metabolic network is in disequilibrium. Further, by introducing a new directed centrality measure via an extension of the subgraph centrality metric to directed networks, we are able to characterise individual metabolites by their participation within metabolic pathways. To demonstrate these ideas, we study 116 metabolic networks of bacteria. In particular, we find that the equilibrium constant for the metabolic networks decreases significantly in-line with variability in bacterial habitats, supporting the view that environmental variability promotes disequilibriumwithin these biochemical reaction systems

AB - Many of the chemical reactions that take place within a living cell areirreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks display considerable asymmetry. In this paper, we explore possible evolutionary factors pertaining to the reduced symmetry observed in these networks, and demonstrate the important role environmental variability plays in shaping their structural organization. Interpreting the returnability index as an equilibrium constant for a reaction network in equilibrium with a hypothetical reference system, enables us to quantify the extent to which a metabolic network is in disequilibrium. Further, by introducing a new directed centrality measure via an extension of the subgraph centrality metric to directed networks, we are able to characterise individual metabolites by their participation within metabolic pathways. To demonstrate these ideas, we study 116 metabolic networks of bacteria. In particular, we find that the equilibrium constant for the metabolic networks decreases significantly in-line with variability in bacterial habitats, supporting the view that environmental variability promotes disequilibriumwithin these biochemical reaction systems

KW - complexity

KW - metabolic networks

KW - returnability

KW - centrality

KW - statistical mechanics

KW - environmental variability

U2 - 10.1007/s10910-013-0288-7

DO - 10.1007/s10910-013-0288-7

M3 - Article

VL - 52

SP - 675

EP - 688

JO - Journal of Mathematical Chemistry

JF - Journal of Mathematical Chemistry

SN - 0259-9791

IS - 2

ER -